【2.4.1】在线双序列比对

一、psa

目前，使用率最高的是 EMBL 网 站的双序列比对工具( http://www.ebi.ac.uk/Tools/psa )。打开页面，上面有全局比对工具、 局部比对工具、还有基因组比对工具。

Gap 的类型及分值设置

EMBL 比对工具将 gap 分为两种，一种叫“gap 开头(GAP OPEN)”，另一种叫“gap 延长(GAP EXTEND)”(图 1)。gap 开头就是连续的一串 gap 里面打头的那一个，可以当 它是队长。gap 延长就是剩下的那些 gap，也就是队长后面跟着的小兵。默认情况下，gap 开头罚分多，gap 延长罚分少。

二、其他工具

三、案例

测试序列：

>test1
GGAUGAGGUUGGAGUCUGACUACAACUACAAGCUUGAAGCCUUUAGGUUUUAAUUGUUACUUUCCUUUACAAUCAUA
>test2
GGAUGAGGUUGGACUCUGACUACAACUACAAGCUUGCAGCCUUUAGGUUUUAAUUCUUACUUUCCUUUACAAUCAUA

方案1：expasy

https://web.expasy.org/sim/

结果示意：

96.1% identity in 77 residues overlap; Score: 269.0; Gap frequency: 0.0%

test1          1 GGAUGAGGUUGGAGUCUGACUACAACUACAAGCUUGAAGCCUUUAGGUUUUAAUUGUUAC
test2          1 GGAUGAGGUUGGACUCUGACUACAACUACAAGCUUGCAGCCUUUAGGUUUUAAUUCUUAC
                 ************* ********************** ****************** ****

test1         61 UUUCCUUUACAAUCAUA
test2         61 UUUCCUUUACAAUCAUA
                 *****************

方案2 Clustal Omega

https://www.ebi.ac.uk/Tools/msa/clustalo/

test1      GGAUGAGGUUGGAGUCUGACUACAACUACAAGCUUGAAGCCUUUAGGUUUUAAUUGUUAC	60
test2      GGAUGAGGUUGGACUCUGACUACAACUACAAGCUUGCAGCCUUUAGGUUUUAAUUCUUAC	60
           ************* ********************** ****************** ****

test1      UUUCCUUUACAAUCAUA	77
test2      UUUCCUUUACAAUCAUA	77
           *****************

方法3

https://en.vectorbuilder.com/tool/sequence-alignment.html

61
GGAUGAGGUUGGAGUCUGACUACAACUACAAGCUUGAAGCCUUUAGGUUUUAAUUGUUAC
|||||||||||||.||||||||||||||||||||||.||||||||||||||||||.||||
GGAUGAGGUUGGACUCUGACUACAACUACAAGCUUGCAGCCUUUAGGUUUUAAUUCUUAC

UUUCCUUUACAAUCAUA
|||||||||||||||||
UUUCCUUUACAAUCAUA

60

方法四：

https://www.genome.jp/tools-bin/clustalw

test1           GGAUGAGGUUGGAGUCUGACUACAACUACAAGCUUGAAGCCUUUAGGUUUUAAUUGUUAC
test2           GGAUGAGGUUGGACUCUGACUACAACUACAAGCUUGCAGCCUUUAGGUUUUAAUUCUUAC
                ************* ********************** ****************** ****

test1           UUUCCUUUACAAUCAUA
test2           UUUCCUUUACAAUCAUA
                *****************

NCBI

https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch&PROG_DEF=blastn&BLAST_PROG_DEF=blastn&BLAST_SPEC=GlobalAln&LINK_LOC=BlastHomeLink

Query  1   GGATGAGGTTGGAGTCTGACTACAACTACAAGCTTGAAGCCTTTAGGTTTTAATTGTTAC  60
           ||||||||||||| |||||||||||||||||||||| |||||||||||||||||| ||||
Sbjct  1   GGATGAGGTTGGACTCTGACTACAACTACAAGCTTGCAGCCTTTAGGTTTTAATTCTTAC  60

Query  61  TTTCCTTTACAATCATA  77
           |||||||||||||||||
Sbjct  61  TTTCCTTTACAATCATA  77

参考资料

• 山东大学 生物信息学课题组荣誉出品 http://www.crc.sdu.edu.cn/bioinfo 巩晶老师课件
• https://molbiol-tools.ca/Alignments.htm
• https://www.ebi.ac.uk/Tools/msa/